Biphenyl and several plant secondary metabolites (PSM) (carvone, isoprene, limonene, naringin, and coumarin) and surfactant (hydroxypropyl-β-cyclodextrin, (HP-β-CD)) have been shown to improve aerobic polychlorinated biphenyl (PCB) removal by several bacterial species. The objective of this study was to determine whether these treatments also affect PCB removal and microbial community structure in a high organic matter soil (Pahokee soil series with 67% organic matter) and low organic matter soil (Woolper soil series with 6% organic matter), as determined by monitoring changes in PCB levels and phospholipid fatty acids (PLFA) profiles in laboratory microcosms amended with these compounds. Biphenyl enhanced di-chlorinated and tri-chlorinated biphenyl removal in both soils, but PSM did not improve removal of these congeners. On the contrary, HP-β-CD decreased PCB removal when used in combination with biphenyl. Two-way analysis of variance indicated that HP-β-CD significantly increased tetra- and penta-chlorinated biphenyl removal from the high organic matter soil, but not from the low organic matter soil. Principal components analysis of PLFA data indicated that HP-β-CD increased proportions of 18:1ω7c associated with Gram-negative bacteria, but decreased 10me16 and 10me17 lipid associated with Gram-positive bacteria, while biphenyl and PSMs had no detectable effects on soil microbial communities. PCB removal was not correlated to any PLFA. In conclusion, PSM previously shown to enhance PCB removal in soil-free systems were not effective in two divergent soils evaluated in this study, and HP-β-CB had increase, decrease, or no effect on PCB removal depending on types of PCB congeners, soils, and co-amendments.